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Published May 2, 2020 | Version 2.0
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Programmed RNA scaffold for streamlined scRNA-seq in CRISPR

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References

  • Qi, L. S. et al. Repurposing CRISPR as an RNA-guided platform for sequence-specific control of gene expression. Cell 152, 1173-1183, doi:10.1016/j.cell.2013.02.022 (2013).
  • Zetsche, B. et al. Cpf1 is a single RNA-guided endonuclease of a class 2 CRISPR-Cas system. Cell 163, 759-771, doi:10.1016/j.cell.2015.09.038 (2015).
  • Abudayyeh, O. O. et al. C2c2 is a single-component programmable RNA-guided RNA-targeting CRISPR effector. Science 353, aaf5573, doi:10.1126/science.aaf5573 (2016).
  • Maeder, M. L. et al. CRISPR RNA-guided activation of endogenous human genes. Nat Methods 10, 977-979, doi:10.1038/nmeth.2598 (2013).
  • Perez-Pinera, P. et al. RNA-guided gene activation by CRISPR-Cas9-based transcription factors. Nat Methods 10, 973-976, doi:10.1038/nmeth.2600 (2013).
  • Thakore, P. I. et al. Highly specific epigenome editing by CRISPR-Cas9 repressors for silencing of distal regulatory elements. Nat Methods 12, 1143-1149, doi:10.1038/nmeth.3630 (2015).
  • Nishimasu, H. et al. Crystal structure of Cas9 in complex with guide RNA and target DNA. Cell 156, 935-949, doi:10.1016/j.cell.2014.02.001 (2014).
  • Konermann, S. et al. Genome-scale transcriptional activation by an engineered CRISPR-Cas9 complex. Nature 517, 583-588, doi:10.1038/nature14136 (2015).
  • Ma, H. et al. Multiplexed labeling of genomic loci with dCas9 and engineered sgRNAs using CRISPRainbow. Nat Biotechnol 34, 528-530, doi:10.1038/nbt.3526 (2016).
  • Dixit, A. et al. Perturb-Seq: Dissecting Molecular Circuits with Scalable Single-Cell RNA Profiling of Pooled Genetic Screens. Cell 167, 1853-1866 e1817, doi:10.1016/j.cell.2016.11.038 (2016).
  • Jaitin, D. A. et al. Dissecting Immune Circuits by Linking CRISPR-Pooled Screens with Single-Cell RNA-Seq. Cell 167, 1883-1896 e1815, doi:10.1016/j.cell.2016.11.039 (2016).
  • Datlinger, P. et al. Pooled CRISPR screening with single-cell transcriptome readout. Nat Methods 14, 297-301, doi:10.1038/nmeth.4177 (2017).
  • Adamson, B. et al. A Multiplexed Single-Cell CRISPR Screening Platform Enables Systematic Dissection of the Unfolded Protein Response. Cell 167, 1867-1882 e1821, doi:10.1016/j.cell.2016.11.048 (2016).
  • Replogle, J. M. et al. Combinatorial single-cell CRISPR screens by direct guide RNA capture and targeted sequencing. Nat Biotechnol, doi:10.1038/s41587-020-0470-y (2020).
  • Zalatan, J. G. et al. Engineering complex synthetic transcriptional programs with CRISPR RNA scaffolds. Cell 160, 339-350, doi:10.1016/j.cell.2014.11.052 (2015).
  • Dominguez, A. A., Lim, W. A. & Qi, L. S. Beyond editing: repurposing CRISPR-Cas9 for precision genome regulation and interrogation. Nat Rev Mol Cell Biol 17, 5-15, doi:10.1038/nrm.2015.2 (2016).
  • Brinkman, E. K., Chen, T., Amendola, M. & van Steensel, B. Easy quantitative assessment of genome editing by sequence trace decomposition. Nucleic Acids Res 42, e168, doi:10.1093/nar/gku936 (2014).
  • Shechner, D. M., Hacisuleyman, E., Younger, S. T. & Rinn, J. L. Multiplexable, locus-specific targeting of long RNAs with CRISPR-Display. Nat Methods 12, 664-670, doi:10.1038/nmeth.3433 (2015).
  • Deo, R. C., Bonanno, J. B., Sonenberg, N. & Burley, S. K. Recognition of polyadenylate RNA by the poly(A)-binding protein. Cell 98, 835-845, doi:10.1016/s0092-8674(00)81517-2 (1999).
  • You, Y., Moreira, B. G., Behlke, M. A. & Owczarzy, R. Design of LNA probes that improve mismatch discrimination. Nucleic Acids Res 34, e60, doi:10.1093/nar/gkl175 (2006).
  • Lim, J. et al. Mixed tailing by TENT4A and TENT4B shields mRNA from rapid deadenylation. Science 361, 701-704, doi:10.1126/science.aam5794 (2018).
  • Fu, Y. et al. High-frequency off-target mutagenesis induced by CRISPR-Cas nucleases in human cells. Nat Biotechnol 31, 822-826, doi:10.1038/nbt.2623 (2013).
  • Hill, A. J. et al. On the design of CRISPR-based single-cell molecular screens. Nat Methods 15, 271-274, doi:10.1038/nmeth.4604 (2018).
  • Mefferd, A. L., Kornepati, A. V., Bogerd, H. P., Kennedy, E. M. & Cullen, B. R. Expression of CRISPR/Cas single guide RNAs using small tRNA promoters. RNA 21, 1683-1689, doi:10.1261/rna.051631.115 (2015).
  • Xu, L., Zhao, L., Gao, Y., Xu, J. & Han, R. Empower multiplex cell and tissue-specific CRISPR-mediated gene manipulation with self-cleaving ribozymes and tRNA. Nucleic Acids Res 45, e28, doi:10.1093/nar/gkw1048 (2017).
  • Knapp, D. et al. Decoupling tRNA promoter and processing activities enables specific Pol-II Cas9 guide RNA expression. Nat Commun 10, 1490, doi:10.1038/s41467-019-09148-3 (2019).
  • Zhang, Y. et al. A gRNA-tRNA array for CRISPR-Cas9 based rapid multiplexed genome editing in Saccharomyces cerevisiae. Nat Commun 10, 1053, doi:10.1038/s41467-019-09005-3 (2019).
  • Xie, K., Minkenberg, B. & Yang, Y. Boosting CRISPR/Cas9 multiplex editing capability with the endogenous tRNA-processing system. Proc Natl Acad Sci U S A 112, 3570-3575, doi:10.1073/pnas.1420294112 (2015).
  • Chen, H. et al. Efficient, continuous mutagenesis in human cells using a pseudo-random DNA editor. Nat Biotechnol 38, 165-168, doi:10.1038/s41587-019-0331-8 (2020).
  • Nielsen, S., Yuzenkova, Y. & Zenkin, N. Mechanism of eukaryotic RNA polymerase III transcription termination. Science 340, 1577-1580, doi:10.1126/science.1237934 (2013).